+Open data
-Basic information
Entry | Database: PDB / ID: 1bkh | ||||||
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Title | MUCONATE LACTONIZING ENZYME FROM PSEUDOMONAS PUTIDA | ||||||
Components | MUCONATE LACTONIZING ENZYME | ||||||
Keywords | MUCONATE CYCLOISOMERASE / MUCONATE LACTONIZING ENZYME / MUCONATE CYCLOISOMERASE AROMATIC HYDROCARBONS CATABOLISM / ISOMERASE | ||||||
Function / homology | Function and homology information chloromuconate cycloisomerase activity / muconate cycloisomerase activity / amino acid catabolic process / : / manganese ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hasson, M.S. / Schlichting, I. / Moulai, J. / Taylor, K. / Barrett, W. / Kenyon, G.L. / Babbitt, P.C. / Gerlt, J.A. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase. Authors: Hasson, M.S. / Schlichting, I. / Moulai, J. / Taylor, K. / Barrett, W. / Kenyon, G.L. / Babbitt, P.C. / Gerlt, J.A. / Petsko, G.A. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bkh.cif.gz | 219.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bkh.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bkh ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bkh | HTTPS FTP |
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-Related structure data
Related structure data | 1mle S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39878.594 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CATB / Plasmid: PKK223-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 References: GenBank: 607908, UniProt: Q51958*PLUS, muconate cycloisomerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.2 Details: MUCONATE LACTONIZING ENZYME (MLE; 5-10 MG/ML) WAS DIALYZED AGAINST 0.2 MM MNCL2, 7 MM MERCAPTOETHANOL, 50 MM TRIS (PH 7), AND CIS, CIS-MUCONATE WAS ADDED TO A FINAL CONCENTRATION OF 0.2 MM. ...Details: MUCONATE LACTONIZING ENZYME (MLE; 5-10 MG/ML) WAS DIALYZED AGAINST 0.2 MM MNCL2, 7 MM MERCAPTOETHANOL, 50 MM TRIS (PH 7), AND CIS, CIS-MUCONATE WAS ADDED TO A FINAL CONCENTRATION OF 0.2 MM. CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY SITTING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 70 MM NACL, 70 MM SODIUM ACETATE (PH 5.2), 0.25% POLYETHYLENE GLYCOL (AVERAGE MOLECULAR WEIGHT 3350). DROPS CONTAINED EQUAL VOLUMES (10 MICRO L) OF WELL SOLUTION AND MLE., vapor diffusion - sitting drop Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 58765 / % possible obs: 70 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.1→2.22 Å / Mean I/σ(I) obs: 2 / % possible all: 36.1 |
Reflection | *PLUS % possible obs: 70 % / Num. measured all: 219744 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED MODEL THAT WAS SOLVED BY MOLECULAR REPLACEMENT USING 1MLE AS A MODEL 1mle Resolution: 2.1→5 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 1
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Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.22 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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